Zhiye Tang

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        Postdoctoral Researcher at University of California, Riverside

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Ph.D. with broad and deep knowledge in chemical and biological processes, necessary mathematics and physics; Expertise in modeling binding processes and their thermodynamics and kinetics; Adept at applying and developing methods that solve problems in categories of non-bonding interaction and biological processes; acknowledged by supervisors and colleagues for professionalism, commitment to excellence, demonstrated ability to communicate and collaborate, and well prepared mentorship for the juniors; able to handle multiple projects; productive even under pressure; self-motivated and experienced in both independent and collaborative projects; outstanding in scientific presentations and good in scientific writings.


University of California, Riverside

Postdoctoral Researcher                                                                                                              Sept 2016-Present

Graduate Research Assistant                                                                                                       Sept 2011-Aug 2016

Research theme: 

        Modeling Molecular Recognition from Thermodynamics to Kinetics: 

        Affinity, Selectivity, Binding Rates and Binding Pathways


1. Novel Dissociation Pathway Search Method Inspired by Principal Component Analysis

2. Thermodynamics and Kinetics Calculations of β-Cyclodextrin and Guest Binding Process

3. Study of CDK8-Ligand Binding Affinities and Dissociation Pathways

4. Explanation of Selective Binding of Various Surfactants on Silver nano-Plate Facets

5. Study of Inhibitor MitoBloCK-10 Resistance on TIM44 Protein and Its Mutants

6. Catalytic Efficiency of Salmonella Tryptophan Synthase (TRPS) and Its Homologue BX1 in Maize


  Ph.D. in Chemistry

  University of California, Riverside                             

  September 2011-August 2016


  Bachelor of Science in Chemistry

  Wuhan University                    

  September 2007-June 2011


Facet Selectivity of Ligands on Silver Nanoplates: Molecular Mechanics Study

Journal of Physical Chemistry C, 2014

Systematic Dissociation Pathway Searches Guided by Principal Component Modes

Journal of Chemical Theory and Computation, 2017

Understanding Ligand-Receptor Non-Covalent Binding Kinetics Using Molecular Modeling

Frontiers in Bioscience, 2016

Binding Thermodynamics and Kinetics Calculations Using Chemical Host and Guest: A Comprehensive Picture of Molecular Recognition


Energy Barriers, Molecular Motions, and Residence Time in Ligand Dissociation: A Computational Study on Type II Inhibitors Binding to CDK8/CycC


A Molecular Dynamics Investigation of CDK8/CycC and Ligand Binding: Conformational Flexibility and Implication in Drug Discovery


Adaptation of a Genetic Screen Reveals an Inhibitor for Mitochondrial Protein Import Component Tim44

The Journal of Biological Chemistry, 2017

A QM/MM Study of Biomimetic Catalysis of Diels-Adler Reactions Using Cyclodextrins


Evaluating the Accuracy of the Umbrella Sampling Plots with Different Dissociation Paths, Conformational Changes, and Structure Preparation


Computer Based Skills

Computational and Modeling Software: 

Molecular/Brownian Dynamics:

AMBER, NAMD, Metadynamics, GaMD, GeomBD, NAM

Conformational Search/Docking:

Autodock, Autodock Vina, VDock, Mining Minima 2

Protonation State Determination:

MCCE, ProPKa, DelPhiPKa

Free Energy Calculation:

Umbrella Sampling (WHAM), Milestoning 

Visualization and Modeling:

Vega ZZ, Avogadro, VMD, PyMol 


Cambridge Crystallographic Data Centre, PDB Data Bank, Pfam 


In House Packages, Personal Analysis Library and Tools 

Programming Languages: 


C++, VC, Fortran, Basic, Mathematica, Direct X, Intel MKL Library 



General Software:

Microsoft Office, 3DS MAX, PHOTOSHOP


English                                          Full Professional Proficiency 

Chinese                                        Native 

Japanese                                      Full Conventional Proficiency/Professional Sufficiency

Last update: Sept 1, 2017